The shocking scale of sexual and physical abuse in educational institutions in Ireland run by the Catholic church was revealed today in a report describing how thousands of boys and girls were raped, abused and exploited by the religious brothers and nuns who were supposed to look after them.

The 2,600-page report by Ireland's Commission to Inquire Into Child Abuse found that for decades rape was "endemic" in more than 250 Irish Catholic care institutions from the 1930s to the 1990s, and that the church in Ireland protected paedophiles in its ranks from arrest.

"A climate of fear, created by pervasive, excessive and arbitrary punishment, permeated most of the institutions and all those run for boys. Children lived with the daily terror of not knowing where the next beating was coming from," it said.

Children in industrial schools and reformatories were treated more like convicts and slaves than people with human rights, it said. Rape was particularly common in boys homes and industrial schools run by the Christian Brothers.

There were angry scenes outside the hotel in Dublin where the report was launched this afternoon after about 20 former residents of industrial schools were prevented from attending the press conference. Speaking outside the hotel, John Kelly of the Irish Survivors of Child Abuse group, Soca, said: "We were treated as criminals as children when we were sent to these places and even now … there were Garda officers on call to arrest us if we tried to get in [to the press conference]. It was an absolute disgrace."

Kelly described the failure of the report to recommend criminal prosecutions as a complete whitewash.

The five-volume report confirmed allegations from thousands of former pupils from the institutions. The Ryan Commission said that beatings in institutions run by both priests and nuns were commonplace. "In some schools a high level of ritualised beating was routine ... Girls were struck with implements designed to maximise pain and were struck on all parts of the body," the report said.

It also criticised the failure of the Irish state, most notably the department of education, for allowing the abuse and exploitation to continue for decades. The department aided this culture "through infrequent, toothless inspectors" that always deferred to the Catholic's church's authority, the report said. The inspections even failed to ensure that children were adequately fed, clothed and educated.

The commission proposed 21 ways the Irish government could recognise past wrongs, including building a permanent memorial, providing counselling and education to victims and improving child protection services.

After the revelations of systematic clerical abuse, Pope Benedict was challenged to hold a Vatican inquiry into the role of Catholic religious orders in Ireland's orphanages and industrial schools. Irish Soca said it was now up to the Vatican to investigate the scandal further.

Kelly said: "Now that the Ryan commission is finished we call upon Pope Benedict to convene a special consistory court to fully investigate the activities of Catholic religious orders in Ireland. Among other things, such a court could establish the whereabouts of Irish state assets that were misappropriated over many years by the religious orders and make restitution to the Irish state exchequer."

Kelly said Irish Soca was disappointed that members of the religious orders who abused children, and the government officials who turned a blind eye to abuse in places like the Artane industrial school, would not be prosecuted.

The commission investigated more than 100 schools run by Catholic religious orders – the majority by the Christian Brothers and Sisters of Mercy.

The commission's original judge, Justice Mary Laffoy, resigned from her post in 2003 over claims that the department of education, which was in charge of inspecting the orphanages and industrial schools, was holding back documents from her inquiry.

Nine-tenths of the bill for compensating victims of the institutionalised abuse will be shouldered by Irish taxpayers rather than the church. In June 2002, a special deal between the Catholic hierarchy and the government of Bertie Ahern, agreed that the Church would pay only €128m in compensation. The overall cost of compensation, according to official figures, will be €1.3bn.

A second damning report, due to be published by the end of June, will detail the abuse of hundreds of children in the Dublin archdiocese from 1940 onwards. More than 100 priests are facing allegations and 400 people have been identified as victims.